Posts

FAQ

Error for region (...) LinAlgError('SVD did not converge')

2021-07-23 PredictDB Team
𝕆ne step of the summary imputation, the computation of snp covariance matrix inverse, is performed via singular value decomposition (SVD). Numerical solutions to the SVD algorithm are not guaranteed to converge, and fail on some regions. When this happens, unmeasured zscores will not be present in … Read more →
FAQ

Error No intersection between model names in MetaXcan Results and Prediction Models

2021-07-23 Festus
𝕋his error happen when the strings captured from the metaxcan results and models don’t coincide A good example is when the metaxcan results' captured names looked like Aorta while the models' captured names looked like Artery_Aorta, this will result into this error […] … Read more →

BrainXcan Brain Feature Prediction Models

2021-07-22 Yanyu Liang
𝕊-BrainXcan takes GWAS as input and return the association between GWAS phenotype and a list of brain image-derived phenotypes. BrainXcan manuscript link. Software documentation (Quick start) link. BrainXcan database link. Analysis scripts link. […] The software is built upon both Python and … Read more →

I need help and these FAQ doesn't cover my issue!

2021-07-21 PredictDB Team
𝔸: You can ask questions at the Google Group: predixcanmetaxcan@googlegroups.com Read more →
FAQ

AttributeError 'NoneType' object has no attribute 'groups'

2021-07-21 Festus
𝕋his error happens when using the Multixcan tool, it usually happens when the tool cant find files in the Metaxcan folder you provided. Thus halting the process of meta analyzing the results. The most probable cause of this error are; […] –metaxcan_filter … Read more →
FAQ

Can I predict genes on chromosome X or Y?

2021-07-21 PredictDB Team
ℕot at the moment. Sex chromosome genes need to be handled differently than those on the autosomes, and do not fit into our existing analysis pipeline. Read more →
FAQ

Error low % of SNPs used

2021-07-21 Festus
𝕋here are different reasons where you could get a low % of SNPs in the model used with your individual level data or summary stats file. Some of the issues include; […] Little overlap between the model SNPs and genotype/summary stats SNPs […] Incomplete/malformed models .db file … Read more →

GTEx v8 models on eQTL and sQTL

2021-07-21 PredictDB Team
𝕎e have produced different families of prediction models for sQTL and eQTL, using several prediction strategies, on GTEx v8 release data. We recommend MASHR-based models below. Elastic Net-based are a safe, robust alternative with decreased power. […] Expression and splicing prediction models … Read more →
FAQ

How can I build my own prediction model?

2021-07-21 PredictDB Team
𝔽or elastic net models, you can find a tutorial here(https://github.com/hakyimlab/PredictDB-Tutorial) The newer GTEx v8 models were generaed with code available here. The documentation is still a work in progress, don’t hesitate to use the PrediXcan/MetaXcan Google Group to ask for support. Read more →
FAQ

How do I query the prediction model db?

2021-07-21 PredictDB Team
𝕋he .db files are simple sqlite files. You can programmatically query them via python, R, perl, etc (using appropriate libraries). Find example queries in this link(https://github.com/hakyimlab/PrediXcan/blob/master/Software/query-db.Rmd) Read more →